MHAP specifications


Unique identifier OMICS_13515
Alternative name MinHash Alignment Process
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Long read sequences, a tab-delimited file of repetitive k-mers
Input format FASTA, DAT
Output data Overlaps in a format similar to BLASR’s M4 format
Biological technology Pacific Biosciences
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Version 2.1.1
Stability Stable
Requirements JDK, Apache Maven
Maintained Yes



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  • person_outline Sergey Koren <>

Publication for MinHash Alignment Process

MHAP institution(s)
Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA; Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA; Invincea Labs, Arlington, VA, USA; National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA; Pacific Biosciences of California, Inc., Menlo Park, CA, USA
MHAP funding source(s)
This work was partly funded under Agreement No. HSHQDC-07-C-00020 awarded by the Department of Homeland Security Science and Technology Directorate (DHS/S&T) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center.

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